User: lkmklsmn

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lkmklsmn820
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4 months, 2 weeks ago
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5 years, 6 months ago
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Posts by lkmklsmn

<prev • 93 results • page 1 of 10 • next >
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Order of reads in FASTQ file
... Hi biostars, FASTQ files contain sequencing reads 'as they come off the sequencing instrument' (https://genome.ucsc.edu/ENCODE/fileFormats.html#FASTQ). Is there any particular order to them? E.g. based on the position of the flow cell? Quality? Thanks in advance. ...
fastq rna-seq written 19 months ago by lkmklsmn820 • updated 19 months ago by Brian Bushnell16k
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Comment: C: ribosomal RNA contamination
... Thanks! Its true that some of the samples had low RINs. Is there any way to correct for this? And still use the samples. As of right now, PCA clustering does not reveal my treatment structure and I am worried these samples are unusable. ...
written 21 months ago by lkmklsmn820
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ribosomal RNA contamination
... Hi, I am working on a RNAseq data set of about 20 human tissue samples. However, some of the samples have a very low alignment rate (~30-40%) while the rest has a a decent alignment rate around 80%. I aligned the reads using STAR with default settings. The log file tells me that for those samples ...
rnaseq rrna contamination written 21 months ago by lkmklsmn820 • updated 21 months ago by Devon Ryan85k
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Total RNA RNA-seq database
... Hi, I am looking for some sort of database/compilation of RNA-seq data that allows me to quickly search by RNA-extraction protocol. More particular, I am interested in ALL GEO deposited RNA-seq datasets which extracted total RNA (as opposed to polyadenylated extraction protocols). Is there are lis ...
extraction protocol rna-seq written 22 months ago by lkmklsmn820 • updated 5 months ago by Biostar ♦♦ 20
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Comment: C: Ribosomal RNA in RNA-seq data
... Thanks. Yes the percentage of multi-mapping reads is very high in those affected samples. Given that only a subset of the samples are affected by this (Alignment rate<50%) my conclusion is that there must have been some error in the rRNA depletion step. ...
written 22 months ago by lkmklsmn820
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Ribosomal RNA in RNA-seq data
... Hi biostars, I am analyzing RNA-seq data (not for the first time) but for a subset of samples I am getting a very low alignment rate (~30%). To find out what is going on I have looked at some of the unaligned reads and they seem to come from ribosomal RNA. Now my question: Are ribosomal RNA sequ ...
rrna mapping rna-seq ribosomal written 22 months ago by lkmklsmn820
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Answer: A: Kallisto New RNA-seq quantification method discussion
... I find the pseudo alignment approach (kallisto, salmon, sailfish) very innovative. However, I would like to point out that RNA-seq data carries a lot more information than just gene expression levels. In my opinion the gene-level output of RNA-seq data is an alignment and not just an expression esti ...
written 2.5 years ago by lkmklsmn820
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IGV zoom into alignment
... I am using IGV to look at some RNA-seq alignment. In general I find this tool extremely helpful. However, when looking at some longer genes I am unable to visualize the alignment and I receive the message: "Zoom in to see alignment". Is there a way to change this setting to visualize the entire ge ...
rna-seq igv written 2.5 years ago by lkmklsmn820 • updated 2.5 years ago by igor6.8k
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Answer: A: How to add a new column with consecutive integer number in a bed file?
... From the command line: seq 1 n | paste bedfile - > bedfileWithInteger ...
written 2.5 years ago by lkmklsmn820
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Download ICGC gene expression data
... Can I download gene expression data from ICGC? If so, how? Do I need controlled access? ...
icgc gene expression download cancer written 2.6 years ago by lkmklsmn820 • updated 2.5 years ago by zlira70

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Popular Question 19 months ago, created a question with more than 1,000 views. For Fragment length Distribution
Epic Question 19 months ago, created a question with more than 10,000 views. For Star Or Tophat?
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Convert IMPUTE2 to VCF while keeping phase information
Popular Question 19 months ago, created a question with more than 1,000 views. For Download ICGC gene expression data
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Great Question 19 months ago, created a question with more than 5,000 views. For Fragment length Distribution
Popular Question 19 months ago, created a question with more than 1,000 views. For Any tools to quantify intron retention in RNAseq data?
Popular Question 19 months ago, created a question with more than 1,000 views. For How to convert IMPUTE2 to VCF format
Popular Question 19 months ago, created a question with more than 1,000 views. For Convert STAR sjdb to gtf
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Fast Rna-Seq Exon Count Calculation
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